captain stern discovered the sea floor cavern and they moved to the sea floor cavern and are hidden there.
You must go to metor falls and see team magma and professor cosmo, then team aqua will come and then they will all leave. Go to mt chimney and the gate should be unlocked
TEAM MAGMA GOES TO THEIR HIDEOUT IN THE JAGGED PASS.TEAM AQUA GOES TO SLATEPORT CITY TO STEAL CAPT STERN'S SUBMARINE.
team aqua has a kyogre and team magma has a groudon first you go to team aqua base and battle kyogre and team then you go to team magma base and battle groudon
there is a cave north in the water. go in there and defeat team aqua.
go to slateport and go to the place where they are working on the submarine and you will see a crowd the crowd will leave and go talk to the scientists waiting then team aqua people will come steal the submarine then go back to lilycove and you will be let in finally
First talk to one of the mecanics in the ship building place. He will tell you to find Cap. Stern. Then go to the museum and talk to Cap. Stern that is on the upper floor. Two Team Aqua members will arrive. You will need to defeat them. Then the Team Aqua leader arrives and talks. Leave and Team Aqua will be gone.
It's just a blocked cavern after it, can't go in there. So if you want the Master ball, take it when Team Aqua is there.
You beat team aqua in the place where everthing is blocked of but you need a shovel
go to mt.pyre, after that, go to slateport city, then go to the aqua hideout..
somewhere under the sea. KEEP ON TRUCKIN UNTIL YOU FIND IT!
If you are talking about the wailmers in the water near the team aqua base you first must go to mount pyre and beat all the team aqua grunts and talk to archie. he will then leave with the red orb. then you must go to slateport town and talk to Captain stern and then team aqua will steal the sumarine then go to team aqua's current base and go through it and beet the admin and when the submarine leaves go back outside and the wailmers should be gone.
go to the ship town then they will be at the shipyard. first you see a scientist then you see team aqua going back to their base and there you go
dive where you see a very huge diving spot, then, you will find a door , go in it, then go up you will be in seafloor cavern which is where team aqua is
you have to go to their hideout.
you go to mount. chimney go down the side and a new cave will open up and it is a team magma hide out when you beat them go to saleport then when team aqua takes the submarine got back to team aqua hideout and beat them then they will go away also team aqua hideout is where you get a masterball
Go to the shipyard and talk to the man right ahead of you when you walk in, once you do that, team aqua will be gone.
you go to slateport city and go to the place where the boat is and you will see a group of people. go inside and you will see the boss. then go back to lilycove and go to team aqua's hideout and you can go inside.
go to slateport and go to the harbour
go to team magma's base after you get the magma emblem magma's base is at the route next to fiery path then beat team magma in there then go to team aqua hideout then when you talk to the team aqua members they will say that their boss is at slateport city at the ferry harbor when you go there team aquas boss will steal their submarine then when you go to team aquas hideout the guys won't be blocking anymore
Go to slateport city and visit the crowd then come back and visit the aqua base.
You have to go to Solopotis where u have to use dive to go up the submarine is there
Go out to the sea!
go into shoal cave and defeat team aqua
you go to SLATEPORT HARBOR
Mt. ChimneySlateport City.Mt. PyroAqua Hideout.Aqua Cavern.